Genome assembly and population genomics of Saxifraga tombeanensis

Saxifraga tombeanensis is an endangered endemic species found in the Prealps of Lombardy, Veneto and Trentino-Alto Adige. It grows on rocky substrates at altitudes between 1,000 and 1,800 meters and is listed as “Endangered” on the IUCN Red List due to its limited distribution and the increasing pressures on its habitat. The European Union, through the LIFE funding program, co-financed the LIFE SEEDFORCE project (https://lifeseedforce.eu) to enhance the conservation status of twenty-nine plant species listed in Annex II of the Council Directive 92/43/EEC (Habitats Directive). The scope of the initiative is to employ an integrated conservation strategy to rescue and enhance populations of endangered native Italian flora. Given its precarious status, S. tombeanensis has been selected as one of twenty-nine target species in the LIFE SEEDFORCE project. To date, no reference genome is available and no studies have assessed genetic diversity of S. tombeanensis. With the aim of filling this knowledge gap, this thesis contributes to the ambitious goals of the LIFE Seedforce project by focusing on the genetic under pinnings of S. tombeanensis conservation. The primary objectives of this research were: • De Novo assembly and quality assessment of the S. tombeanensis assembly, including gene annotation. • Population genomics analysis to investigate the genetic diversity and population structure of the species. A genome-wide genotyping approach was used which involves the double digestion of DNA with restriction enzymes (ddRAD-seq) to investigate the genetic structure of S. tombeanensis. In this study, 123,632 Single Nucleotide Polymorphisms (SNPs) were identified across the genome of S. tombeanensis. Genetic analyses showed in general low levels of heterozygosity and relatively low levels of kinship and inbreeding in all eight study populations. Analysis of the genetic structure showed that the populations were not highly differentiated from each other. Admixture analyses revealed that the TOM population is the only one with admixed individuals. These findings offer important insights into the genetic diversity of this species, supporting the development of conservation strategies aimed at enhancing population resilience and ensuring long-term survival.